Enzyme structure and functioning Flashcards
1
Q
What are enzymes?
A
Biological catalyst that lowers the activation energy
2
Q
What kind of proteins are most enzymes?
A
Globular
3
Q
What are all metabolic processes catalysed by?
A
Enzymes
4
Q
Are enzymes specific catalysts?
A
Yes
5
Q
What is the substrate?
A
The molecule or atom that an enzyme acts on
6
Q
What is substrate transformed into?
A
Product
7
Q
Why are biocatalysts better than inorganic catalysts?
A
More effective
Greater specificity (avoids side products)
Milder reaction conditions
Higher reaction rate
Capacity for regulation
8
Q
Can active sites of enzymes recognise stereoisomers?
A
Yes
9
Q
What do proteolytic enzymes do?
A
Catalyse the hydrolysis of peptides and also the hydrolysis of an ester bond
10
Q
Do different enzymes have different degrees of specificity?
A
Yes they do
11
Q
What are cofactors?
A
Small molecules that some enzymes require for activity
12
Q
Two main classes of cofactors
A
Coenzymes (organic molecule derived from vitamin)
Metals
13
Q
What are tightly bound coenzymes called?
A
Prosthetic group
14
Q
What are holoenzymes?
A
Enzymes with its cofactor
15
Q
What are apoenzymes?
A
Enzymes without its cofactor
16
Q
Are there any disorders and deceases that are caused by deficiency of one enzyme or excessive activity of an enzyme?
A
Yes both
17
Q
Can enzymes be used therapeutically?
A
Yes
18
Q
Do many drugs act through interactions with enzymes
A
Yes
19
Q
What are isoenzymes?
A
Same catalytic action and same name (like exokinese) but there are more variants (like I II III …) which are produced by different organs
20
Q
6 major classes of enzymes
A
Oxidoreductases
Transferases
Hydrolases
Lyases (synthases)
Isomerases
Ligases (synthetases)
21
Q
What do transferases do?
A
Transfer groups
22
Q
What do hydrolyses do?
A
Use water to break proteins
23
Q
What do lyases?
A
Fuse two molecules to form one molecule
24
Q
What do isomerases do?
A
Transfer isomers, move groups
25
What are ligases?
Uses energy to fuse two molecules together
26
5 types of enzyme regulations
Allosteric regulation
Reversible covalent modifications
Proteolytic cleavage
Feedback regulation
Regulation by isoenzymes
27
What is the allosteric site?
Site that is different from the binding site
28
Can feedback regulation be positive or negative?
Both
29
Can allosteric regulation be positive or negative?
Both
30
What is the rate of enhancement?
How much the enzymes enhances the reaction compared to without the enzymes
31
Is the tertiary structure of a protein destabilised by the hydrophobic effect?
No
32
Where does the strength of alpha kreatin protein come from?
Cross-linking alpha helices by disulfide bonds
33
The motif in the glycolysis enzyme hexokinase could contain what?
Beta turn
Beta sheet
Alpha helix
Disulfide bonds
34
What feature is not associated with globular proteins?
Alpha and beta classification
35
What characteristics of protein is associated with proteostasis?
Synthesis
Refolding
Degradation
36
What does denaturing followed ny renaturing of a protein demonstrate?
That primary structure dictates tertiary structure
37
Are chaperones always required?
No
38
What does gibbs free energy provide information about?
Spontaneity and not the rate of reaction
39
What does the Gibbs free energy have to be for a reaction to occur?
Negative
40
What is a reaction called when the gibbs free energy is negative?
Exergonic reaction
41
What is Gibbs free energy when the reaction is at equilibrium?
0
42
What is a reaction called if Gibbs free energy is positive?
Endergonic reaction
43
Do enzymes affect the equilibrium?
No
44
Can enzymes effect the Gibbs free energy of a reaction?
No
45
What is the velocity of a reaction?
Product/time
46
Which has the highest activation state:
Product to substrate
or
Substrate to product
Product to substrate
47
What does enzymes do to lower the activation energy?
Organise the reactive groups into close proximity and proper orientation
48
What do enzyme bind best?
Transition states
49
Does speed matter when it comes to enzymes?
Yes speed matters a lot
50
What is binding energy?
Major source of free energy used by enzymes to lower the activation energies of reactions
51
Common features of active sites of enzymes
3d cleft or crevice created by AA from different parts of the primary structure
Active site constitutes a small portion of the enzyme volume
Unique microenvironment
Multiple weak interactions take place between enzyme and substrate
specificity depends on the molecular architecture at the active site
52
Does the specificity of an enzyme effect the rate of reaction?
Not necessarily
53
Is the ligand binding site and active site the same?
Yes, both connect with substrate and change into a product
The ligand binding site is a part of the active site
54
4 factors contributing to the barrier to reaction
Entropy of molecules in solution
Salvation shell of hydrogen bonded water
The distortion of substrates that must occur in many reaction
The need for proper alignment of catalytic functional group
55
What kind of energy can be used to overcome all the barriers contributing to the reaction barrier?
Binding energy
56
What is the desolvation of the substrate?
Removing of molecules surrounding substrate
57
What is acid-base catalysis?
Give and take protons
58
What is covalent catalysis?
Change reaction paths
59
What is metal ion catalysis?
Use redox cofactor, pKa, shifters
60
3 kinds of catalysis
Acid-base
Metal ion
Covalent
61
Are enzymes specific for a particular substrate?
Generally yes
62
Difference between number of products produced by an enzyme and a nonbiological catalyst
An enzymes yields a specific product where nonbiological catalyst may produce more than one product because of side reactions
63
Effects of enzymes on reaction
Activation energy lowered
Formation of transition state is promoted
Rate constant for reverse reaction increases
64
2 ways enzymes increase the rate of reaction
Lower the activation energy of the reaction
Promote the formation of a transition state
65
Difference between lock and key and induced fit model
In induced fit the conformation changes when the substrate binds where in lock and key the structure is rigid
66
2 things both the induced fit and lock and key model have in common
The substrate binds at the active site, forming an enzyme-substrate complex
The substrate binds to the enzyme through non covalent interactions
67
What inorganic ion does not serve as a cofactor?
Ca2+
68
What is an apoenzyme?
An enzyme that requires a cofactor for its activity
69
What is the inorganic ion called when it is very tightly or covalently bound by the enzyme?
A prosthetic group
70
Is polymerases one of the 7 EC classes of enzymes?
No
71
What is the free energy starting point for a reverse reaction designated as?
Ground state
72
Why is the conversion of sucrose to CO2 not spontaneous?
Because it has a very large activation energy barrier
73
What does an enzyme change relative to an uncatalyzed reaction?
The rate of the reaction
74
Can small changes in free energy lead to large changes in the equilibria?
Yes
75
What a reaction where the rate depends on the concentration of two molecules called?
Second-order reaction
76
Binding energy is defined as
The energy derived from non covalent enzyme-substrate interaction
77
What is the primary source of the energy enzymes used to reduce activation energies?
Noncovalent enzyme-substrate intercation
78
How does the induced fit mechanism of enzyme catalysis work?
The enzyme undergoes a conformational change to maximise weak interactions to the substrate
79
Which amino acid has the least effect on the function of an enzyme if it replaces a Glu residue in the enzyme?
Asp
80
True or false: does covalent catalysis by enzymes never involve coenzymes?
False
81
What does it mean that enzymes can be stereoselective?
They can be so elective they distinguish L-amino acids and D-amino acids
82
What do proteolytic enzymes catalyse?
The hydrolysis of peptide bonds
83
2 bonds proteases bread
Peptide bonds
Ester bonds
84
2 proteolytic enzymes
Trypsin
Thrombin
85
Do trypsin and thrombin have the same specificity?
No
86
During which state does the enzymes bind most tightly?
Transition state
87
Which amino acid residue is especially agressive in acid-base catalysis?
Serine
88
What does covalent catalysis require on the enzyme?
A nucleophile
89
Examples of nucleophiles used in covalent catalysis
Serine
Thiolate
Amine
Carboxylate
90
What is chymotrypsin?
A peptidase
91
Can one enzyme use multiple enzymatic mechanisms?
Yes
